RetrogeneDB ID: retro_vvin_150

Retrocopy location

• Organism: Grape (Vitis vinifera)
• Coordinates: 4:21462372..21462912(-)
• Located in intron of: VIT_04s0044g00590

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: None
• Ensembl ID: VIT_00s0179g00190
• Aliases: None
• Description: None

Sequence

>retro_vvin_150
AGGCACGGACTGACAGGGTCTGATGCAGAGAAATCCAATTCGCTTTTAGGAGATGCTCTTCAACAAATTTATTTAGCACG
AGTACCAATTATGAAATGTGGAGAATGATGATAAAGTTCAACTGGCAACTTTGATAGAAGACGTTCAAACGCCTGCATTT
TGGAGACAAAAACACTTGTTTCTACTAACTTATGGATGACCAGTGCTCAAGCTAGATCAAGTGCTCACTACGATCCACAC
CATAATCTTCTATGCATAATTGATGGCTGCAAGCAAGTTGTTTTATTTCCCTCTCTACAAGTCTCTTGTTATATCCAATG
CCTATATATGGAGAGGCCTCAAACCATAATTCTGTGGCTTTAGAGGAAACCTGATTTTTCAATTCAGCCAAGAGCCGAAC
ACTCAACGAAGCACTCTCTGAAGGCCATTCTTCATGCAGAAGACGCACTGTTCATTCTTGAAAGCCGGTTCCATCAAGTG
GATAATAATGATATGGCTATTGCTGTTAGTTTCTGGTGGCGGTCAAACATAATGTCCAGC

Alignment

ORF - retro_vvin_150 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.07 %
• Parental protein coverage: 56.25 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  RHGLAGSDAEQSNSLLGDAPQQIYLAQVPIM-NVENDDKVQLATLIEDIQTPAF-LETKTLASINLWMNS
          RHGL.GSDAE.SNSLLGDA.QQIYLA.VPIM.NVENDDKVQLATLIED.QTPAF.LETKTL.S.NLWM.S
Retrocopy RHGLTGSDAEKSNSLLGDALQQIYLARVPIM>NVENDDKVQLATLIEDVQTPAF<LETKTLVSTNLWMTS

Parental  AQARSSTHYDPHHNLLCIIAGCKQVVLWPP-SASPLLYPMPIYGEASNHSSVALED-PDFSIHPRAEHSM
          AQARSS.HYDPHHNLLCII.GCKQVVL.P..S.S.LLYPMPIYGEASNH.SVALE..PDFSI.PRAEHS.
Retrocopy AQARSSAHYDPHHNLLCIIDGCKQVVLFPS<STSLLLYPMPIYGEASNHNSVALEE>PDFSIQPRAEHST

Parental  KHSQKVILHAGDALFIPEGWFHQVDSNDLTIAVNFWWRSNITSS
          KHS.K.ILHA.DALFI.E..FHQVD.ND..IAV.FWWRSNI.SS
Retrocopy KHSLKAILHAEDALFILESRFHQVDNNDMAIAVSFWWRSNIMSS

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Vitis vinifera was not studied using RNA-Seq expression data.

ChIP-Seq

Vitis vinifera was not studied using ChIP-Seq data.

EST

Vitis vinifera was not studied using EST data.

TSS

Vitis vinifera was not studied using FANTOM5 data.

Lab

retro_vvin_150 was not experimentally validated.

Homology

Retrocopy orthology:

Vitis vinifera does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Vitis vinifera	VIT_00s0179g00190	3 retrocopies	retro_vvin_150 , retro_vvin_170, retro_vvin_43,